FastSurfer QuickSeg doesn't work with OASIS `.img` files about fastsurfer

[m-reuter]

You would first need to convert the .img file to a nifti or mgz file. One way to do this is using mri_convert (from FreeSurfer, it is also part of our container, so you could change the --entrypoint or run interactively with bash).
mri_convert input.img output.mgz

[FahimFBA]

You would first need to convert the .img file to a nifti or mgz file. One way to do this is using mri_convert (from FreeSurfer, it is also part of our container, so you could change the --entrypoint or run interactively with bash). mri_convert input.img output.mgz

Thank you. It is kind of awkward as it didn't work earlier.

I found the issue that caused the error earlier. You must need to have the corresponding .hdr (Header) file to convert them using FreeSurfer. Earlier, I reorganized the dataset, and in the process, I deleted the header files without having any idea of their importance. Therefore, FreeSurfer, FSL, nibabel, simpleitk also failed to convert them.

If you have the corresponding .hdr files, then FreeSurfer can convert them into .mgz or .nii perfectly.

However, I managed to batch-process them nicely using Brainder.. Then I can easily incorporate them into FastSurfer.

I am also closing this issue keeping the comments as others might find them useful.

[dkuegler]

Technically, Fastsurfer should be able to use any file format that is compatible with nibabel. We just always use mgz and nifty, so our official support is only for those two.